Genetic Variant SLC28A1:p.Gln456Gln (chr15-84935179-A-G) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_004213.5(SLC28A1):c.1368A>G(p.Gln456Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.88 in 1,613,972 control chromosomes in the GnomAD database, including 626,315 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.89 ( 61089 hom., cov: 31)

Exomes 𝑓: 0.88 ( 565226 hom. )

Consequence

SLC28A1
NM_004213.5 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.228

Variant links:

Genes affected

SLC28A1 (HGNC:11001): (solute carrier family 28 member 1) Enables azole transmembrane transporter activity; cytidine transmembrane transporter activity; and uridine transmembrane transporter activity. Involved in azole transmembrane transport; nucleoside transport; and pyrimidine-containing compound transmembrane transport. Located in cytosol; nuclear speck; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

SLC28A1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 15-84935179-A-G is Benign according to our data. Variant chr15-84935179-A-G is described in ClinVar as [Benign]. Clinvar id is 3060136.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-0.228 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.941 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC28A1	NM_004213.5 link	c.1368A>G	p.Gln456Gln	synonymous_variant	Exon 14 of 19	ENST00000394573.6	NP_004204.3	O00337-1B7Z3L5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
SLC28A1	ENST00000394573.6 link	c.1368A>G	p.Gln456Gln	synonymous_variant	Exon 14 of 19	1	NM_004213.5	ENSP00000378074.1	O00337-1
SLC28A1	ENST00000286749.3 link	c.1368A>G	p.Gln456Gln	synonymous_variant	Exon 13 of 18	1		ENSP00000286749.3	O00337-1
SLC28A1	ENST00000538177.5 link	c.1084-8266A>G		intron_variant	Intron 11 of 14	2		ENSP00000443752.1	B7Z3L6

Frequencies

GnomAD3 genomes

AF:

0.895

AC:

136043

AN:

152056

Hom.:

61029

Cov.:

show subpopulations

Gnomad AFR

AF:

0.948

Gnomad AMI

AF:

0.938

Gnomad AMR

AF:

0.863

Gnomad ASJ

AF:

0.934

Gnomad EAS

AF:

0.956

Gnomad SAS

AF:

0.936

Gnomad FIN

AF:

0.827

Gnomad MID

AF:

0.953

Gnomad NFE

AF:

0.869

Gnomad OTH

AF:

0.894

GnomAD3 exomes

AF:

0.885

AC:

222499

AN:

251446

Hom.:

98702

AF XY:

0.885

AC XY:

120248

AN XY:

135898

show subpopulations

Gnomad AFR exome

AF:

0.949

Gnomad AMR exome

AF:

0.858

Gnomad ASJ exome

AF:

0.935

Gnomad EAS exome

AF:

0.960

Gnomad SAS exome

AF:

0.929

Gnomad FIN exome

AF:

0.826

Gnomad NFE exome

AF:

0.867

Gnomad OTH exome

AF:

0.882

GnomAD4 exome

AF:

0.879

AC:

1284588

AN:

1461798

Hom.:

565226

Cov.:

AF XY:

0.880

AC XY:

639758

AN XY:

727212

show subpopulations

Gnomad4 AFR exome

AF:

0.951

Gnomad4 AMR exome

AF:

0.860

Gnomad4 ASJ exome

AF:

0.935

Gnomad4 EAS exome

AF:

0.959

Gnomad4 SAS exome

AF:

0.929

Gnomad4 FIN exome

AF:

0.828

Gnomad4 NFE exome

AF:

0.871

Gnomad4 OTH exome

AF:

0.893

GnomAD4 genome

AF:

0.895

AC:

136164

AN:

152174

Hom.:

61089

Cov.:

AF XY:

0.895

AC XY:

66567

AN XY:

74372

show subpopulations

Gnomad4 AFR

AF:

0.949

Gnomad4 AMR

AF:

0.863

Gnomad4 ASJ

AF:

0.934

Gnomad4 EAS

AF:

0.956

Gnomad4 SAS

AF:

0.936

Gnomad4 FIN

AF:

0.827

Gnomad4 NFE

AF:

0.869

Gnomad4 OTH

AF:

0.895

Alfa

AF:

0.880

Hom.:

106342

Bravo

AF:

0.898

Asia WGS

AF:

0.934

AC:

3248

AN:

3478

EpiCase

AF:

0.870

EpiControl

AF:

0.867

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

SLC28A1-related disorder

Benign:1

Oct 30, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

2.2

DANN

Benign

0.50

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over